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If your Nikkor lens is the
AF-S NIKKOR 80-400mm f/4.5-5.6G ED VR
then with that teleconverter, it is listed as 'AF Not Possible' with a TC-20EII, on this page:
It is surprising, given this indication, that the lens Auto-Focuses in any setting at all.
But it appears that the limitation is owing to incompatibility, as listed.
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You might want to try cleaning the contacts, on both the lens assembly and the camera lens mount, or the teleconverter if it has lens contacts, with a clean dry lint-free rag cloth, rubbing the contacts gently only, lest the coating on the contacts be rubbed off.